Differential methylation level of cpg loci that are determinative of kidney cancer

Abstract

The present disclosure provides for and relates to the identification of novel biomarkers for diagnosis and prognosis of kidney cancer. The biomarkers of the invention show altered methylation levels of certain CpG loci relative to normal kidney tissue, as set forth.

We claim: 
     
         1 . A method for determining the presence or absence of kidney cancer in an individual, the method comprising:
 a. identifying an individual in need of the prevention or treatment of kidney cancer;   b. obtaining a biological sample from the individual and isolating the DNA therefrom;   c. determining the methylation level of at least one cytosine within a DNA region in a sample from the individual where the DNA region is at least 90% identical to a sequence selected from the group consisting of SEQ ID NOS: 1, 4, 6, 7, 8, 11, 12, 13, 14, 17, 20, 21, 22, 23, and 24; and   d. comparing the methylation level of the at least one cytosine to a threshold value for the at least one cytosine, wherein the threshold value distinguishes between individuals with and without kidney cancer, wherein the comparison of the methylation level to the threshold value is predictive of the presence or absence of kidney cancer in the individual.   
     
     
         2 . The method of  claim 1  wherein said sample is a biopsy sample. 
     
     
         3 . The method of  claim 1  wherein said sample is a blood sample. 
     
     
         4 . The method of  claim 1  wherein said sample is a urine sample. 
     
     
         5 . The method of  claim 1  wherein the methylation level of at least 3 DNA regions are determined. 
     
     
         6 . The method of  claim 1  wherein the methylation level of at least 5 DNA regions are determined. 
     
     
         7 . A kit for determining the presence or absence of kidney cancer in an individual, the kit comprising:
 a. a plurality of nucleic acid primers configured to bind to a nucleic acid at least 90% identical to a sequence selected from the group consisting of SEQ ID NOS.: 1, 4, 6, 7, 8, 11, 12, 13, 14, 17, 20, 21, 22, 23, and 24;   b. wherein the primers are for use in a polymerase chain reaction (PCR) reaction;
 wherein the primers are configured to aid in the determination of the methylation level of at least one cytosine within the nucleic acid. 
   
     
     
         8 . The method of  claim 7  wherein the nucleic acid is at least 92% identical to a sequence selected from the group consisting of SEQ ID NOS.: 1, 4, 6, 7, 8, 11, 12, 13, 14, 17, 20, 21, 22, 23, and 24. 
     
     
         9 . The method of  claim 7  wherein the nucleic acid is at least 95% identical to a sequence selected from the group consisting of SEQ ID NOS.: 1, 4, 6, 7, 8, 11, 12, 13, 14, 17, 20, 21, 22, 23, and 24. 
     
     
         10 . The method of  claim 7  wherein the methylation level of at least 3 nucleic acids is determined. 
     
     
         11 . A method for determining the presence or absence of clear cell renal cell carcinoma in an individual, the method comprising:
 a. identifying an individual in need of the prevention or treatment of kidney cancer;   b. obtaining a biological sample from the individual and isolating the DNA therefrom;   c. determining the methylation level of at least one cytosine within a DNA region in a sample from the individual where the DNA region is at least 90% identical to a sequence selected from the group consisting of SEQ ID NOS: 2, 9, 10, 15, 19, 25, 26 and 27; and   d. comparing the methylation level of the at least one cytosine to a threshold value for the at least one cytosine, wherein the threshold value distinguishes between individuals with and without kidney cancer, wherein the comparison of the methylation level to the threshold value is predictive of the presence or absence of kidney cancer in the individual.   
     
     
         12 . The method of  claim 11  wherein said sample is a biopsy sample. 
     
     
         13 . The method of  claim 11  wherein said sample is a blood sample. 
     
     
         14 . The method of  claim 11  wherein said sample is a urine sample. 
     
     
         15 . The method of  claim 11  wherein the methylation level of at least 3 DNA regions are determined. 
     
     
         16 . A kit for determining the presence or absence of clear cell renal cell carcinoma in an individual, the kit comprising:
 a. a plurality of nucleic acid primers configured to bind to a nucleic acid at least 90% identical to a sequence selected from the group consisting of SEQ ID NOS.: 2, 9, 10, 15, 19, 25, 26 and 27;   b. wherein the primers are for use in a polymerase chain reaction (PCR) reaction;
 wherein the primers are configured to aid in the determination of the methylation level of at least one cytosine within the nucleic acid. 
   
     
     
         17 . The method of  claim 7  wherein the nucleic acid is at least 92% identical to a sequence selected from the group consisting of SEQ ID NOS.: 2, 9, 10, 15, 19, 25, 26 and 27. 
     
     
         18 . The method of  claim 7  wherein the nucleic acid is at least 95% identical to a sequence selected from the group consisting of SEQ ID NOS.: 2, 9, 10, 15, 19, 25, 26 and 27. 
     
     
         19 . A method for determining the presence or absence of at least one of kidney cancer or clear cell renal cell carcinoma in an individual, the method comprising:
 a. identifying an individual in need of the prevention or treatment of kidney cancer;   b. obtaining a biological sample from the individual and isolating the DNA therefrom;   c. determining the methylation level of at least one cytosine within a DNA region in a sample from the individual where the DNA region is at least 90% identical to a sequence selected from the group consisting of SEQ ID NOS: 3, 5, 16 and 18; and   d. comparing the methylation level of the at least one cytosine to a threshold value for the at least one cytosine, wherein the threshold value distinguishes between individuals with and without kidney cancer, wherein the comparison of the methylation level to the threshold value is predictive of the presence or absence of kidney cancer in the individual.